Align acetolactate synthase (subunit 1/2) (EC 2.2.1.6) (characterized)
to candidate 5209297 Shew_1775 acetolactate synthase 3 regulatory subunit (RefSeq)
Query= BRENDA::P00894 (163 letters) >FitnessBrowser__PV4:5209297 Length = 164 Score = 235 bits (599), Expect = 3e-67 Identities = 114/163 (69%), Positives = 141/163 (86%) Query: 1 MRRILSVLLENESGALSRVIGLFSQRGYNIESLTVAPTDDPTLSRMTIQTVGDEKVLEQI 60 MRRI+SVLLEN+ GALSRV+GLFSQRGYNIESLTVAPTDD TLSR+ I V DE VLEQI Sbjct: 1 MRRIISVLLENQPGALSRVVGLFSQRGYNIESLTVAPTDDVTLSRLNITLVADEAVLEQI 60 Query: 61 EKQLHKLVDVLRVSELGQGAHVEREIMLVKIQASGYGRDEVKRNTEIFRGQIIDVTPSLY 120 EKQLHKL+D+L+VS + + +H+ERE+ L+K++A G GR+EVKR +IFRGQI+DVT LY Sbjct: 61 EKQLHKLIDILKVSNITESSHIERELALIKVKAKGAGREEVKRTADIFRGQIVDVTSELY 120 Query: 121 TVQLAGTSGKLDAFLASIRDVAKIVEVARSGVVGLSRGDKIMR 163 T+Q+AGTS KLDAF+A+I +V K++EV+RSGVVGL RG+K MR Sbjct: 121 TIQMAGTSDKLDAFIAAIGEVTKVIEVSRSGVVGLCRGEKAMR 163 Lambda K H 0.318 0.136 0.360 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 132 Number of extensions: 1 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 163 Length of database: 164 Length adjustment: 18 Effective length of query: 145 Effective length of database: 146 Effective search space: 21170 Effective search space used: 21170 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 43 (21.2 bits)
Align candidate 5209297 Shew_1775 (acetolactate synthase 3 regulatory subunit (RefSeq))
to HMM TIGR00119 (ilvN: acetolactate synthase, small subunit (EC 2.2.1.6))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00119.hmm # target sequence database: /tmp/gapView.25052.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00119 [M=158] Accession: TIGR00119 Description: acolac_sm: acetolactate synthase, small subunit Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-66 207.7 3.8 5.1e-66 207.6 3.8 1.0 1 lcl|FitnessBrowser__PV4:5209297 Shew_1775 acetolactate synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5209297 Shew_1775 acetolactate synthase 3 regulatory subunit (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 207.6 3.8 5.1e-66 5.1e-66 1 158 [] 1 159 [. 1 159 [. 0.99 Alignments for each domain: == domain 1 score: 207.6 bits; conditional E-value: 5.1e-66 TIGR00119 1 kkhvlsvlvenepGvLsrvsGlfarrgfniesltvgeteekdlsrmtivvegddkvveqiekqleklvdvlkvldlte 78 +++++svl+en+pG+Lsrv+Glf++rg+niesltv+ t++ +lsr+ i++ +d+ v+eqiekql+kl+d+lkv+++te lcl|FitnessBrowser__PV4:5209297 1 MRRIISVLLENQPGALSRVVGLFSQRGYNIESLTVAPTDDVTLSRLNITLVADEAVLEQIEKQLHKLIDILKVSNITE 78 69**************************************************************************** PP TIGR00119 79 seivkrelvlvkvsalgeerneikelteifrgrvvDvsedslivelsgkedkisaflkllkefg.ikevarsGlvals 155 s++++rel+l+kv+a+g r+e+k++++ifrg++vDv+ + ++++++g++dk++af++++ e++ + ev+rsG+v+l lcl|FitnessBrowser__PV4:5209297 79 SSHIERELALIKVKAKGAGREEVKRTADIFRGQIVDVTSELYTIQMAGTSDKLDAFIAAIGEVTkVIEVSRSGVVGLC 156 **************************************************************999************* PP TIGR00119 156 rge 158 rge lcl|FitnessBrowser__PV4:5209297 157 RGE 159 *85 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (158 nodes) Target sequences: 1 (164 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 5.01 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory